Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • fasta to fastq

    Hello guys

    I' m working with TopHat and Bowtie to start my Phaseolus' RNAseq analysis, but to use this protocol I need to convert the cDNA sequences .fasta to .fastq.

    What software can I use?

  • #2
    Normally one would start with NGS data already in fastq format when doing Tophat analysis.

    If you want to convert your fasta sequences to fake fastq then you could use reformat.sh from BBMap like so

    Code:
    $ reformat.sh in=test.fa out=fake.fq qfake=35

    Comment


    • #3
      I would recommend not doing this reformatting approach, or at least proceeding with caution. With FASTA, you can be certain that the quality scores won't be used, but with a fake FASTQ you may be introducing artifacts. That is, unless you can be certain that the quality scores won't be used, but I'm not sure you can force this behavior with these tools.

      For a tool that just needs the sequences there is obviously no harm in going to FASTQ so a parser will work. For an aligner, I'd be cautious since they use quality scores.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X